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Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea

Nature Chemical Biology volume 6, pages 277–282 (2010)Cite this article

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Abstract

A modified base at the first (wobble) position of some tRNA anticodons is critical for deciphering the genetic code. In eukaryotes and eubacteria, AUA codons are decoded by tRNAsIle with modified bases pseudouridine (and/or inosine) and lysidine, respectively. The mechanism by which archaeal species translate AUA codons is unclear. We describe a polyamine-conjugated modified base, 2-agmatinylcytidine (agm2C or agmatidine), at the wobble position of archaeal tRNAIle that decodes AUA codons specifically. We demonstrate that archaeal cells use agmatine to synthesize agm2C of tRNAIle. We also identified a new enzyme, tRNAIle-agm2C synthetase (TiaS), that catalyzes agm2C formation in the presence of agmatine and ATP. Although agm2C is chemically similar to lysidine, TiaS constitutes a distinct class of enzyme from tRNAIle-lysidine synthetase (TilS), suggesting that the decoding systems evolved convergently across domains.

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Figure 1: Identification and determination of the chemical structure of the new modified nucleoside in archaeal tRNAIle2.
Figure 2: Agmatine is a metabolic substrate of agm2C in archaeal cells.
Figure 3: In vitro reconstitution of agm2C formation by A. fulgidus TiaS.
Figure 4: Recognition of the AUA codon by archaeal tRNAIle2 with agm2C.

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Acknowledgements

We are grateful to Y. Sakaguchi, T. Saigo, K. Nishikawa, S. Ohno and Y. Nomura for technical support and many fruitful discussions. Special thanks are due to Thermo Fischer Scientific for FT-MS analysis. This work was supported by Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports, and Culture of Japan (to Tsutomu Suzuki, T.Y. and T.W.); by a Japan Society for the Promotion of Science Fellowship for Japanese Junior Scientists (to Y.I.); by a PRESTO program grant from Japan Science and Technology (to T.N.) and by a grant from the New Energy and Industrial Technology Development Organization (NEDO) (to Tsutomu Suzuki).

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Authors and Affiliations

  1. Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan

    Yoshiho Ikeuchi, Satoshi Kimura, Takeo Suzuki & Tsutomu Suzuki

  2. Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan

    Tomoyuki Numata

  3. Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan

    Tomoyuki Numata

  4. Department of Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan

    Daigo Nakamura & Takashi Yokogawa

  5. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan

    Toshihiko Ogata & Takeshi Wada

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  1. Yoshiho Ikeuchi
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Contributions

Y.I. determined the chemical structure of agm2C. S.K. performed biochemical studies of agm2C and TiaS. Takeo Suzuki performed in vivo labeling of agm2C. T.N. performed expression and purification of TiaS. D.N. purified native tRNA under the supervision of T.Y. T.O. supported chemical synthesis of agm2C under the supervision of T.W. All authors discussed the results and commented on the manuscript. Tsutomu Suzuki designed and supervised all the work.

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Correspondence to Tsutomu Suzuki.

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The authors declare no competing financial interests.

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Supplementary Methods and Supplementary Figures 1–9 (PDF 2310 kb)

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Ikeuchi, Y., Kimura, S., Numata, T. et al. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol 6, 277–282 (2010). https://doi.org/10.1038/nchembio.323

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